Question: Assembly of 454 raw data (in fastq)
0
gravatar for bird77
7 months ago by
bird7720
bird7720 wrote:

I need to assemble raw reads from a project that already has been published. The metagenome was sequenced with 454, but the files are only present in fastq format.

Is there an assembler which is up-to-date which can assemble long 454 reads with this quality profile? Can UDBA or Megahit deal with that?

Or does anyone have different recommendations?

Thank you for your help.

assembly • 409 views
ADD COMMENTlink modified 7 months ago by colindaven790 • written 7 months ago by bird7720

I thought (though I may well be wrong) that Velvet or SOAP was originally developed for 454 sequencing.

ADD REPLYlink written 7 months ago by jrj.healey6.8k
0
gravatar for colindaven
7 months ago by
colindaven790
Hannover Medical School
colindaven790 wrote:

Newbler always worked pretty well with 454. Otherwise CLC genomics was also easy.

Can Spades deal with it for a more modern option ?

ADD COMMENTlink written 7 months ago by colindaven790

I don't think so. I use SPAdes fairly frequently and never noticed any information suggesting it does, but I am guessing a bit.

ADD REPLYlink written 7 months ago by jrj.healey6.8k
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